Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex

Abstract

Nuclear LIM-only (LMO) and LIM-homeodomain (LIM-HD) proteins have important roles in cell fate determination, organ development and oncogenesis. These proteins contain tandemly arrayed LIM domains that bind the LIM interaction domain (LID) of the nuclear adaptor protein LIM domain-binding protein-1 (Ldb1). We have determined a high-resolution X-ray crystal structure of LMO4, a putative breast oncoprotein, in complex with Ldb1-LID, providing the first example of a tandem LIM:Ldb1-LID complex and the first structure of a type-B LIM domain. The complex possesses a highly modular structure with Ldb1-LID binding in an extended manner across both LIM domains of LMO4. The interface contains extensive hydrophobic and electrostatic interactions and multiple backbone-backbone hydrogen bonds. A mutagenic screen of Ldb1-LID, assessed by yeast two-hybrid and competition ELISA analysis, identified key features at the interface and revealed that the interaction is tolerant to mutation. These combined properties provide a mechanism for the binding of Ldb1 to numerous LMO and LIM-HD proteins. Furthermore, the modular extended interface may form a general mode of binding to tandem LIM domains.

The LIM-only factor LMO4 regulates expression of the BMP7 gene through an HDAC2-dependent mechanism, and controls cell proliferation and apoptosis of mammary epithelial cells

“…To test whether Clim and LMO4 can form a complex on the BMP7 promoter, we performed double ChIP assays in the MCF7-LMO4-TetOff cells, first precipitating the tagged LMO4 with a Myc antibody and then the endogenous Clim2 protein with a Clim2 antibody. Under conditions of high LMO4 expression, Clim antibody could precipitate the LMO4 complex on the BMP7 promoter (Figure 4c, lane 6), indicating that both LMO4 and Clim2 bind to the BMP7 promoter, most likely in a complex given the high-affinity interaction between these proteins (Deane et al, 2004;Ryan et al, 2006). These results are specific because the Clim2 antibody was not able to precipitate IgG-precipitated BMP7 promoter (Figure 4c, lane 5).…”

In silicodesign of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations

“…'GGGS' was a better linker than 'AAY' for multi-epitope vaccines in eliciting immune responses. G-rich linkers have the capacity to improve sequence flexibility without affecting the function of proteins they attach to, 39,40 while the AAY linker, as the cleavage site of proteasomes in mammalian cells, helps form natural epitopes and prevent the formation of 'junctional epitopes', which enhanced epitope presentation. Unexpectedly, however, linker AAY induced large changes in protein characteristics, including hydrophilicity, flexibility, a region, b region, turn region, and coil region, all of which could influence protein stability, and reduce less immunogenicity.…”

Solution structure of a tethered Lmo2LIM2/Ldb1LID complex

“…Together these parameters indicate that the solution structure of Lmo2 LIM2 -Ldb1 LID is of medium to high resolution. 24 The structure of this tethered complex closely resembles that of other LIM-Ldb1 LID complexes, 22,23,[25][26][27] [e.g. Fig.…”